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- EMDB-32050: Al-bound structure of the AtALMT1 mutant M60A -

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Basic information

Entry
Database: EMDB / ID: EMD-32050
TitleAl-bound structure of the AtALMT1 mutant M60A
Map data
SampleAl-bound protein sample of the AtALMT1 mutant M60A:
Aluminum-activated malate transporter 1 / (ligand) x 2
Function / homologymalate transmembrane transporter activity / malate transmembrane transport / Aluminum-activated malate transporter / Aluminium activated malate transporter / plant-type vacuole membrane / response to aluminum ion / integral component of membrane / plasma membrane / Aluminum-activated malate transporter 1
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsWang J
Funding support China, 9 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0908501 China
Ministry of Science and Technology (MoST, China)2018YFA0508100 China
Ministry of Science and Technology (MoST, China)2016YFA0501100 China
National Natural Science Foundation of China (NSFC)31870724 China
National Natural Science Foundation of China (NSFC)82030108 China
National Natural Science Foundation of China (NSFC)31872796 China
National Natural Science Foundation of China (NSFC)81571127 China
National Natural Science Foundation of China (NSFC)31730006 China
National Natural Science Foundation of China (NSFC)31600606 China
CitationJournal: Cell Res / Year: 2022
Title: Structural basis of ALMT1-mediated aluminum resistance in Arabidopsis.
Authors: Jiangqin Wang / Xiafei Yu / Zhong Jie Ding / Xiaokang Zhang / Yanping Luo / Ximing Xu / Yuan Xie / Xiaoxiao Li / Tian Yuan / Shao Jian Zheng / Wei Yang / Jiangtao Guo /
Abstract: The plant aluminum (Al)-activated malate transporter ALMT1 mediates the efflux of malate to chelate the Al in acidic soils and underlies the plant Al resistance. Here we present cryo-electron ...The plant aluminum (Al)-activated malate transporter ALMT1 mediates the efflux of malate to chelate the Al in acidic soils and underlies the plant Al resistance. Here we present cryo-electron microscopy (cryo-EM) structures of Arabidopsis thaliana ALMT1 (AtALMT1) in the apo, malate-bound, and Al-bound states at neutral and/or acidic pH at up to 3.0 Å resolution. The AtALMT1 dimer assembles an anion channel and each subunit contains six transmembrane helices (TMs) and six cytosolic α-helices. Two pairs of Arg residues are located in the center of the channel pore and contribute to malate recognition. Al binds at the extracellular side of AtALMT1 and induces conformational changes of the TM1-2 loop and the TM5-6 loop, resulting in the opening of the extracellular gate. These structures, along with electrophysiological measurements, molecular dynamic simulations, and mutagenesis study in Arabidopsis, elucidate the structural basis for Al-activated malate transport by ALMT1.
History
DepositionOct 14, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateDec 1, 2021-
Current statusDec 1, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.019
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.019
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7voj
  • Surface level: 0.019
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_32050.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 180 pix.
= 182.52 Å
1.01 Å/pix.
x 180 pix.
= 182.52 Å
1.01 Å/pix.
x 180 pix.
= 182.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density
Contour LevelBy AUTHOR: 0.019 / Movie #1: 0.019
Minimum - Maximum-0.10789047 - 0.15441944
Average (Standard dev.)-8.028117e-05 (±0.005481161)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 182.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z182.520182.520182.520
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.1080.154-0.000

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Supplemental data

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Sample components

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Entire Al-bound protein sample of the AtALMT1 mutant M60A

EntireName: Al-bound protein sample of the AtALMT1 mutant M60A / Number of Components: 4

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Component #1: protein, Al-bound protein sample of the AtALMT1 mutant M60A

ProteinName: Al-bound protein sample of the AtALMT1 mutant M60A / Recombinant expression: No
MassExperimental: 120 MDa
SourceSpecies: Arabidopsis thaliana (thale cress)
Source (engineered)Expression System: Homo sapiens (human) / Vector: pEZT-BM / Cell of expression system: HEK-293
Source (natural)Location in cell: cell membrane / Organ Or Tissue: root

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Component #2: protein, Aluminum-activated malate transporter 1

ProteinName: Aluminum-activated malate transporter 1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 56.773551 kDa
SourceSpecies: Arabidopsis thaliana (thale cress)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: ligand, ACETIC ACID

LigandName: ACETIC ACID / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 6.005199999999999405 MDa

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Component #4: ligand, ALUMINUM ION

LigandName: ALUMINUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.698199999999999705 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 6 mg/mL / pH: 5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 277.15 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 64 e/Å2 / Illumination Mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C2 (2 fold cyclic) / Number of Projections: 216946
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3 Å / Resolution Method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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